General questions

What does "Gerris" mean?

Gerris is the Latin (and French) name of the water strider (or water
boatman), an aquatic insect which uses surface tension to "walk" on
the surface of the water. Have a look at the logo on the front page of
the Gerris web site for a
graphical description.

How is "Gerris" pronounced?

With a soft `g' like `genetics' or `general'.

Where are the printable versions of the docs?

What grid generator is Gerris using?

Gerris uses an "embedded boundary" technique. Grid generation reduces
to the computation of the "shape" (surface and volume fractions) of
Cartesian (cubic) cells cut by the solid boundaries. These "boolean
operations" between solids are performed automatically using GTS (the
GNU Triangulated Surface Library). The cells cut by the boundaries can
then be refined automatically using the quad/octree structure of the
discretisation. Mesh generation is entirely automatic and works for
any input geometry (provided it is topologically consistent, i.e. an
orientable non-self-intersecting manifold).

Can Gerris handle unstructured tetrahedral meshes?

Are there any plans to extend Gerris to RANS (Reynolds-Averaged Navier-Stokes)?

The focus is on time-dependent Navier-Stokes, so RANS is not really in
my mind but nothing is in the way if this is what you need.

Large Eddy Simulation (LES) models is what I am thinking about as far
as turbulence modelling is concerned.

What boundary conditions are in the code now and what BCs are planned for the near future?

Slip, no-slip solid boundaries, inflow, outflow, periodic..., but
everything is there to implement your own boundary conditions as
Gerris can not supply all the boundary conditions users could think
of.

How is Gerris parallelised? Does it use MPI or a shared memory technique?

Gerris uses a domain decomposition approach using MPI for
synchronisation at domain boundaries. For the moment it does not do
dynamic balancing of domain sizes which limits its applicability to
statically refined problems.

Does adaptive refinement work in parallel?

Yes but there may be load-balancing issues. I
don't use the MPI version for the moment. For the type of studies I am
interested in, it is usually much easier to do "direct parallelism"
i.e. run several simulations with different parameters "in parallel".

Does the parallel version of the code do load-balancing?

No, the code does not have parallel load-balancing capabilities at the
moment. It can do static load-balancing i.e. "optimal" partitioning of
the domain so that an initial mesh is divided in roughly equal-sized
subdomains while minimising the size of the communication boundaries.

I don't personally use the parallel capability of the code very
much. What I usually need is several different sequential computations
with a different set of parameters. This is of course the ideal case
for "parallelism". I don't usually require to run "one shot" very
large parallel computations.

When will parallel load-balancing be available?

Load-balancing is not very high on my list of priorities at the
moment. I don't see fundamental obstacles to dynamic
load-balancing. The main limitation of the current code which would be
hard to do away with is the fact that only "coarse grain" parallelism
is possible (i.e. domains can be partitioned only at the GfsBox level
not at an individual cell level). This is a limitation only when the
ratio of total number of cells to total number of CPUs becomes small
however.

What's ultimately needed to implement "full" load-balancing is a way
in the code to transfer entire GfsBoxes from one processor to the
other (ensuring the correct restructuring of associated boundary
conditions). This is a technical problem but which could be solved
relatively easily by someone with a good understanding of the code
structure at the GfsBox/GfsBoundary level.

An intermediate possibly easier (but not as clean) solution can be to
save the simulation and stop the code when load-balancing becomes too
bad, then do a static load-balancing step and restart a "new"
simulation with this as initial state. I would probably first
experiment with this approach to get used to the problems involved
first and then move to the full internally-coded solution.

Can Gerris handle moving/deforming solid geometries?

Can Gerris also be used for compressible fluids?

No, but this would be possible. The existing shallow-water solver in particular
can be seen as one form of compressible flow solver.

Can Gerris solve the shallow-water (Saint-Venant) equations?

Yes, starting with version 0.6.0, although I would not consider it
ready for "general consumption" right now. For simple examples on how
this works have a look at the shallow-water test cases.

How can I assist you in your development effort?

Thanks for asking. The easiest way you can help me is first by using
the code. Setting up your own test cases etc... And reporting
problems, either in term of usability, unexpected results etc...

By doing that you will certainly help me ensure that the code is as
robust as possible and you will soon find areas which need improvement
and which you might like to work on (preferably after consultation with
me so that we can coordinate our efforts).

An important point is also to remember to try to send your
questions/comments to one of the two Gerris mailing lists (gfs-users
or gfs-devel) so that other people can benefit from the exchange (I
will also more readily reply to a message on the mailing list than to
one addressed directly to me).

Installation and coding

How do I install the parallel version of Gerris?

If when running ./configure you got lines looking like

checking for mpicc... yes

then you don't have anything else
to do. Otherwise, you need to make sure that you have MPI installed
and that the mpicc command is in your PATH.

Is there a Mac version of Gerris?

Are there any plans to release a more documented version of the code?

I have chosen the "classical" point of view that, if the general
description of the arguments and of what the function does (given just
before the body of (almost) all the exported functions) together with
the code in the function itself does not clearly describe what the
function is doing, then this is a problem with the code itself not
with the documentation. A counter-example of that would be a very long
monolithic code described by comments every few lines.

Also, from my personal experience, working with a number of research
and commercial codes, I would consider Gerris to be fairly well documented.
The code is also quite modular, so you shouldn't (hopefully) need to
go through all the 16000 lines of code...

Of course, I would be glad to address any detailed problem you may
have (unclear documentation etc...)

Are there any plans to release a C++/Java/Object Oriented implementation of Gerris?

No. Gerris is already object-oriented (with class inheritance etc...),
see the tutorial for an example of how this works.

Physics and dimensioning

Where are variables like viscosity, density etc... defined?

By default, the density is unity and the molecular viscosity is
zero (i.e. there is no explicit viscous term in the momentum
equation). In practice, it does not mean that there is no viscosity at
all however, because any discretisation scheme always has
some numerical viscosity. Of course, the lower the numerical
viscosity, the better. Gerris has quite good properties in this
respect.

How come Gerris generates a Von Karman vortex street for an inviscid flow around a half-cylinder? I would expect the inviscid flow to remain irrotational.

This is perfectly right in the case of flow around smooth
solid boundaries. If there is a sharp corner (as for the
half-cylinder), the potential flow solution is singular in the sense
that the velocity tends to infinity as one gets closer to the
corner. In practice (finite difference numerical solution) and in
reality, the local numerical (or real) viscosity near the corner,
smears out the singularity, which results in the creation of a (point)
source of vorticity which is then carried away by the mean flow (as
you can see on the half-cylinder example).

Even in the case of a smooth geometry, numerical inaccuracies in the
boundary conditions on the solid surface can lead to the generation of
a small amount of vorticity (much smaller than what is generated at a
discontinuity though).

How would I create a 5x5 box?

It is possible to change the size of the unit GfsBox, however, I would
encourage you to think in "relative units" rather than "absolute
units". When studying fluid mechanics (and other physical) problems it
is almost always a good idea to use non-dimensional units. This makes
relevant independent parameters (such as the Reynolds number for
example) immediately apparent. When using Gerris I would recommend
scaling all your physical input parameters by a reference length (the
physical length of the GfsBox). This also eliminates the need for
changing the length of the GfsBox.

How would I modify the file you sent me (tangaroa.gfs) for a ship that is 150 meters long and exposed to a cross-flow wind velocity of 50 meters/sec?

You would have to non-dimensionalise both the model ship geometry and wind speed.

Let's say you want the ship to occupy one third of a GfsBox, the reference length of the GfsBox would then be 3*150 meters, so you would
scale the model geometry by a factor of 1/(reference length) or 1/450.

How would I redimensionalise U,V,W and P?

However, keep in mind that the only relevant parameter for the
(constant density) Navier-Stokes equations is the Reynolds number. If
you do not include any explicit viscous term the (theoretical)
Reynolds number is always infinite. In practice this means that the
inflow velocity has only a uniform scaling influence on the final
solution. For example

simulation 1: inflow velocity set to 1.0

simulation 2: inflow velocity set to 2.0

then, the velocity field of simulation 1 at time t is exactly equal
(to machine precision) to the velocity field for simulation 2 at time
t/2.0, divided by 2.0.

It looks like t and dt output by GfsOutputTime are also scaled? How would I scale t and dt to time in seconds?

How do I scale Vorticity?

The code provides support for the variable density incompressible Euler equations. Does that mean you can input the density of the fluid density (air, water, etc...)?

Not really if what you mean is a constant density throughout the
domain. In the case of the incompressible constant-density Navier-Stokes
equations, the density is irrelevant. It is only a scaling factor for
the pressure.

What this really means is that Gerris can deal with flows where
the density varies across the domain (e.g. a mixture of two miscible
fluids, or density variations due to salinity variations in the sea for
example).

Although the initialised problem is symmetric, the solution becomes asymmetric as time passes, why?

The code is indeed not perfectly numerically symmetrical. This is due
mainly to the tolerance in the solution for the pressure equation, if
you decrease the tolerance you should see smaller
asymmetries. You can do this using

How do I deal with negative values of the pressure?

Your question is interesting, it comes down to the meaning of
"pressure" for incompressible flows.

For compressible flows "pressure" has a thermodynamic definition
and is directly linked to other physical quantities through an
equation of state. It is defined on an absolute scale.

For incompressible flows "pressure" does not have a thermodynamic
definition (there is no equation of state linking it to other physical
quantities), rather it comes about as the stress field necessary to
enforce the incompressibility condition. In this context, only its
gradients are relevant, not its absolute value i.e. one can add any
constant to the pressure field without changing the solution.

Conclusion: If you don't like negative pressures just add any constant
necessary to make them positive.

Representation of solid boundaries

How do I import my geometry into Gerris?

It depends how the geometry is defined. If it has an analytical representation, the easiest is to use implicit surfaces. Have a look at the GfsSolid and GfsSurface documentations.

If the geometry was created using a CAD package, you need to convert it into a set of triangulated surfaces
and be able to export it in the GTS format (very simple, described
here)
or alternatively in the STL format (which can be converted to GTS
using the stl2gts program).

The tricky bit is that the surfaces you export must represent proper
solid objects i.e. they must be orientable, closed, manifold and non
self-intersecting surfaces. Note that this is an issue only for explicit surfaces.

What CAD package can I use to export STL/GTS files?

Blender can do that and is open-source, also have a look at ac3d, k3d
and Pro/Engineer, Rhino. There are plenty of others.

If your STL file is ASCII (not binary) make sure that it is not DOS-formatted. You can convert from DOS to Unix ASCII formatting using:

% dos2unix myfile.stl

Do I need to tessellate (increase the number of triangles of) my surface before importing it into GTS?

If your solid boundary is exactly defined using a few triangles, there
is no need to use more. In short, the mesh size generated by Gerris is
completely independent from the "triangle size" of the input surface
(in contrast to what happens in "classical" unstructured mesh
solvers).

If for example, you want to resolve the boundary layers around your
solid, you could tell Gerris to use a "fine enough" mesh like this:

which tells Gerris to use 10 levels of refinement near the solid
surface. "Fine enough" is going to depend on the details of the
physics (most importantly Reynolds number) and on the constraints in
term of computational time, memory size etc...

Which part of the parameter file tells Gerris where the half-cylinder is placed? How do I alter it?

The position of the solid object is defined (obviously) through the
coordinates of its vertices. If you created it using a CAD or similar
program, you can translate, rotate etc... the object using this same
program.

You can also specify simple transformations (scaling, translations, rotations) directly in the parameter file, have a look at the GfsSurface documentation.

Alternatively, you can use the transform program which comes with
GTS.

% transform -h

will give you a summary of the transformations you can make, currently

Are there any tools for converting format-X (not STL) files (generated via a CAD system) to a GTS-format file?

The GTS file format is described here.
It is very simple. You should be able to write your own filter
using your favourite scripting language. You might want to have a look
at the cleanup utility which comes with GTS (in the examples/
directory) It will allow you to link unlinked faces, remove duplicate
vertices etc...

Gerris seem to allow only one solid body, is this correct?

No, there is no limitation on the number and/or complexity of solid
bodies (as long as they are properly oriented, manifold geometrical
surfaces). Multiple bodies are possible, either as a single GTS file
containing multiple separate bodies or as multiple calls to
GfsSolid in the parameter file with several non-intersecting GTS
surfaces.

How do I orient my solid surfaces properly?

The orientation of the
faces of your solid defines where the fluid side is (by
convention the counter-clockwise (CCW) normal direction to a face points toward the solid
side). If your solid is not oriented properly you can use the flip = 1 option of GfsSurface ot the --revert or -i options of transform to turn it "inside out".

It looks like all STL files need to be turned "inside out". I don't understand why, but transform -i fixed the problem.

It is just a matter of different conventions. The program you use has
chosen to orient the CCW face normals toward the "outside" of the
solid object.

Can solids intersect?

No, you first need to use the "boolean operations" or "constructive
solid geometry" operations of your solid modeller to generate the
union of your solids.

This may change in the future.

We have a problem inserting some GTS files generated from STL files and even inserting the standard GTS files found on the GTS samples site?

The samples files on the GTS site are not
necessarily describing consistent geometric surfaces (i.e. they can be
open, non-manifold etc...)

Generally it is a good idea to check the topology of a GTS surface before trying to import it. This can be done using something like:

If you prefer to use solids created in your CAD package of choice, create a cube with its edges parallel to the X-, Y- and Z-axis. The overall size of the cube is arbitrary, but all edges should be of equal size. If you have this, subtract your pipe's inside from this cube and export the result as STL.

The following shell commands will prepare this STL data for Gerris. The commands are split up for a better understanding, but in practice could be joined together into a shell pipeline.

Post-processing and Visualisation

Is there a way to view the results and solid(s) at the same time (with the solid in the correct location? (Geomview question)

Yes, you need to select the Inspect->Appearance->Normalise->None
option in the Geomview menu. The default is to "normalise"
(i.e. rescale) each object individually (Normalise->Individual option)
so that it fits at the centre of the viewed area.

Is there any way to output U, V, W, P, etc... at point (X, Y, Z) in the flow field?

Where is the description of the format of the data section of saved simulation files?

If you intend to read the simulation files (to convert them or do
other operations/calculations etc...) I would highly recommend that
you do so through the functions provided by the Gerris library
(gfs_simulation_read() and so on). This way you will not reinvent the
wheel and you will be able to use all the functionalities provided by
the library (traversal of the octree structure, computation of
gradients, interpolations etc...). This would also ensure that your
code is independent of the format changes in the simulation file.

Just to give you an example on how this can bite you:

the GfsOutputSimulation object can be used like this (in simulation
files)

in this case, the simulations files (sim-0.1, sim-0.2 etc...) will
only contain the P and C variables.

Your code which reads the simulation files would need to know about
this. The gfs_simulation_read() function deals with that for you and
other functions give you easy access to this kind of information (what
variables where contained in the simulation file etc...)

Also have a look at the code which writes a Gerris simulation as a VTK or Tecplot unstructured file in src/unstructured.c.

The GfsOutputSimulation and GfsOutputLocation files only place up to eight decimals. Is there any way to increase the number of decimal places?

Good question. No there isn't, short of editing and recompiling the
source code. That would be a nice option to have in the simulation
file.

I would like a time-averaged velocity profile, would I have to specify a number of monitoring points at different heights, or is there a method to time average over a line through the solution domain?

There is no method to do line averaging at the moment, however there
is a method which averages (or more exactly stores the sum) of a given
variable in time over the whole domain. You can do it like that:

which would add U to SUx at every timestep (istep = 1) starting from
time 1 (start = 1) etc... and U*U to SU2x at every timestep
etc... The resulting sums are then written at the end of the
simulation in the file simulation-sum. This file can then be
post-processed (using gfs2oogl for example) to obtain averages,
standard deviations etc... (along any curves you want of course).

Using animate, the sequence of images generated by OutputPPM looks weird, what's happening?

This is probably an artefact of the way the animate command
displays a series of PPM images. What happens is that OutputPPM
generates PPM images which are just big enough to contain all the data
in your simulation e.g. if you use 7 levels of refinement and one box,
OutputPPM will generate images with 128x128 pixels. If
you use an adaptive resolution with a maximum level of 6, the size of
the resulting image generated by OutputPPM can be anything in
1x1, 2x2, 4x4, 8x8, 16x16, 32x32, 64x64 depending on the maximum number of
levels necessary to verify your adaptation criterion. As a result,
animate can see a series of PPM images with a variable size, if
you look carefully you will see that the weird patterns you see are
smaller-size images of your simulation, displayed in the top-left
corner of the initial image. What animate should really do is blank
out the previous larger image before displaying the smaller image, to
make the difference in size clear.

The solution is simple, you can set the size of the images generated by OutputPPM using:

which will result in PPM images of size 64x64, independently
of the maximum level of refinement in the simulation.

Why create a new visualisation tool like GfsView? Can't you use existing tools like Mayavi/VTK, OpenDX etc...?

Most visualisation packages assume that the data is defined
on either structured Cartesian meshes (this includes curvilinear
coordinates) or fully unstructured meshes (tetrahedra etc...).

The octrees used by Gerris need first to be converted into
unstructured tetrahedra and then imported into OpenDX etc... This is
quite slow and memory-hungry and loses most of the advantages of
the octree: in particular the multilevel representation of the
solution is very useful from a visualisation point of view.

I am not aware of any good visualisation tool which understands
octrees. It would be a good idea to post messages on OpenDX, Mayavi, VTK
etc... mailing lists asking about support for octrees. I did that and
got little feed back, but more messages would show the developers of these
projects that there is a desire for such a feature.

GfsView makes the most of the octree structure to accelerate
visualisation, computation of isosurfaces etc...

Running Gerris

Are the files vorticity.gfs and half-cylinder.gfs included in the Gerris distribution?

No, you will need to type them following the tutorial...

Your flow analysis for the RV Tangaroa is just the type of problem I would like to be able to solve quickly, etc... How long did it take to setup and run this problem? Could you send me a copy of the input file?

The longest was to get a "proper" CAD model of the vessel. We had it
made by the ship designers but it was full of topological
inconsistencies (folds, degenerate faces etc...). It was a real pain
to fix it. Once you have a proper orientable, manifold solid there is
nothing more to do really.

How do you modify the mesh to give greater detail in a specific area of flow?

As you saw in the tutorial, the meshing is automatic and follows
user-defined criteria. Vorticity and gradient-based criteria for
example, can be used. The level of refinement used for both the
initial refinement and the adaptive refinement can both be functions
of space, time, other variables etc... which give almost total
flexibility. Other criteria can be added within the object-oriented
framework of the code if necessary.

Is there any way to initialise the grid so that a fine grid is generated around the surface of the solid and a coarser grid is generated in the flow field (resulting in significantly fewer cells being generated)?

Is there a way to control the maximum size of a simulation?

the maxcells option tells the adaptive algorithm to use a maximum of
400,000 cells to discretise the domain. When this maximum number is
reached the algorithm minimises the maximum cost of the refinement by
optimally distributing the cells across the domain. You have to be
aware however that this means that the accuracy of the simulation will
not be constant in time.

My simulation file looks fine but does not work, why?

Are you sure your text editor does not
include special characters in your files? (the infamous DOS end of line
comes to mind).

On Mac, traditionally, a text file uses Return (ASCII 13) as an end of line character. Unix uses Line Feed (ASCII 10) as an end of line character. You should thus convert your files if they have such characters. See for instance the osxfaq page

Restarting a simulation always starts at t = 0 ?!?

If you want to re-run a simulation from a later point in simulation time ( t > 0 ), you have to save results into distinct files:

How do I make boundary conditions time-dependent?

What about this page of the tutorial?
As described in the object hierarchy
functions can depend on time (just use variable t). You should
be able to use this to implement your boundary conditions.

How do I run Gerris in parallel?

The principle is relatively simple. Each GfsBox can take a pid
argument which defines the number of the process on which the solution
for this GfsBox will be computed. If you take the "half cylinder"
example and do something like: